Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcctgttacgttcctgagataaagaaaaggagggaaaaaaaccgtttgttgttctgattcgtctttcagactgatatttcaatatttacccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATAATCACGGGTTCAAGACAATCACATCTTTTTCAGACATTTGAGACTAGAT

Basic information

species Vitis vinifera
transcript Vv19s0014g02480.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA13G35120.3 (Glycine max), 3'ss of exon 9
----agcctgttacgttcctgagataaagaaaaggagggaaaaaaaccgtttgttgttctgattcgtctttcagactgatatttcaatatttacccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATAATCACGGGTTCAAGACAATCACATCTTTTTCAGACATTTGAGACTAGAT
         |  |  | |||  |||       |  ||   ||| ||    ||| |  | |  |  |    | |   || |     |  | ||   |  |  |||| |||||||||||||| ||||||||||| ||||||||||| || || || ||||| || ||||||||||||| ||| || || || || | |||| |  |
tgtggtagaggaatttcccttggatcccacttataagaccaaataagaaattgcttattttgtctgcacataaatttgctg----acaaattgttctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACAATCATGGCTTCAAGACAATCAAATCCTTCTCGGAGATCTAAGACCAATT

upper sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 11
-----agcctgttacgttcc-tgagataaagaaaaggagggaaaaaaaccgtttgttgttctgattcgtctttcagactgatatttcaatatttacccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATAATCACGGGTTCAAGACAATCACATCTTTTTCAGACATTTGAGACTAGAT
      |      |  |||| |  |||  |   |       ||| ||    ||  || || ||        | || |   || | |  | | ||| ||  |  |||| |||||||||||||| ||||||||||| ||||||||||| || || || ||||| || ||||||||||||| ||| || || || || | |||  ||  
ggtgtggtagaggaatttccataggatccacttataataccaaataagaaattgcttattttg------tctgcacataaatttgttgacaattatcctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACAATCATGGCTTCAAGACAATCAAATCCTTCTCGGAGATCTAAGATCAGTA

upper sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 11
agcctgtta-cgttcctgagataaagaaaaggagggaaaaaaaccgtttgttgttctgattcgtctttcagactgatatttcaatatttacccat-tggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATAATCACGGGTTCAAGACAATCACATCTTTTTCAGACATTTGAGACTAGAT
||    |||  ||    |  ||||  | ||       ||       |||  | || |  ||   ||||   |   | |||  || | || ||||| |  |||| |||||||||||||| ||| ||||||||||||||| |||||| || || |||||||| |||||||  ||||  || || || || || ||| | |||||
agtacattagtgtgaagggtataagtagaacttctccaacctgttttttaatattttagttatgcttttttatgcacatt--aacaattgcccatgtttcagGCTTGGAGGTGATAATTTCTGTTCGACCAGGAAATGCACCTCTCCCTGAAAATCACGGCTTCAAGATGATCAGTTCCTTCTCTGAGATCTGAAAGTAGAT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|352768679|gb|FQ467891.1|FQ467891
EST:     TTTGTTTGTGACAGATGTCTATCAAGAAGCTGTTGCTGCAAAGGCAGCAG                         GGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA
genomic: TTTGTTTGTGACAGATGTCTATCAAGAAGCTGTTGCTGCAAAGGCAGCAGgtaattagta ... ccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA
EST: gi|29785157|gb|CB341909.2|CB341909
EST:     TTTGTTTGTGACAGATGTCTATCAAGAAGCTGTTGCTGCAAAGGCAGCAG                         GGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA
genomic: TTTGTTTGTGACAGATGTCTATCAAGAAGCTGTTGCTGCAAAGGCAGCAGgtaattagta ... ccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA
EST: gi|110378704|gb|EC943848.1|EC943848
EST:     TTTGTTTGTGACAGATGTCTATCAAGAAGCTGTTGCTGCAAAGGCAGCAG                         GGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA
genomic: TTTGTTTGTGACAGATGTCTATCAAGAAGCTGTTGCTGCAAAGGCAGCAGgtaattagta ... ccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA
EST: gi|32245843|gb|CD711662.1|CD711662
EST:     TTTGTTTGTGACAGATGTCTATCAAGAAGCCGTTGCTGCAAAGGCAGCAG                         GGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA
genomic: TTTGTTTGTGACAGATGTCTATCAAGAAGCTGTTGCTGCAAAGGCAGCAGgtaattagta ... ccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA
EST: gi|110412327|gb|EC978073.1|EC978073
EST:     TTTGTTTGTGACAGATGTCTATCAAGAAGCTGTTGCTGCAAAGGCAGCAG                         GGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA
genomic: TTTGTTTGTGACAGATGTCTATCAAGAAGCTGTTGCTGCAAAGGCAGCAGgtaattagta ... ccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgttctgattcgtctttcagactgatatttcaatatttacccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATAATCACGGGTTCAAGACAATCACATCTTTTTCAGACATTTGAGACTAGAT
                        gactgat  putative branch site (score: 3)
                                        tttaccc  putative PPT
                           tgatatttcaatattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcctgttacgttcctgagataaagaaaaggagggaaaaaaaccgtttgttgttctgattcgtctttcagactgatatttcaatatttacccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATAATCACGGGTTCAAGACAATCACATCTTTTTCAGACATTTGAGACTAGAT

- -ctgttac
- - - - - -ttcctga
- - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - -aaaaaaa